Variant report

Variant	rs10483642
Chromosome Location	chr14:55920460-55920461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10144034	0.81[EUR][1000 genomes]
rs10144130	0.81[EUR][1000 genomes]
rs10150596	0.81[EUR][1000 genomes]
rs10150617	0.81[EUR][1000 genomes]
rs10782426	0.84[CEU][hapmap]
rs12431542	0.80[EUR][1000 genomes]
rs1572613	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs34652660	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4901562	0.82[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes]
rs4901568	0.85[CEU][hapmap]
rs4901570	0.81[EUR][1000 genomes]
rs6573028	0.80[EUR][1000 genomes]
rs6573029	0.81[EUR][1000 genomes]
rs6573031	0.81[EUR][1000 genomes]
rs6573032	0.81[EUR][1000 genomes]
rs713477	0.84[AMR][1000 genomes]
rs7142204	0.85[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs7146170	0.81[EUR][1000 genomes]
rs8009706	0.81[EUR][1000 genomes]
rs8010013	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs8014526	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs8014621	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10483642	WDHD1	cis	parietal	SCAN
rs10483642	FBXO34	cis	cerebellum	SCAN
rs10483642	RPL13AP3	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55912600-55922000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:55913600-55921200	Weak transcription	HSMMtube	muscle
3	chr14:55913600-55925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:55914000-55920600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:55914000-55920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr14:55914000-55921000	Weak transcription	Brain Anterior Caudate	brain
7	chr14:55915200-55920600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:55915400-55920600	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:55915600-55921000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:55915800-55920800	Weak transcription	Fetal Brain Female	brain
11	chr14:55916600-55920600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr14:55917000-55921000	Enhancers	HUVEC	blood vessel
13	chr14:55917000-55921400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr14:55917400-55921000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr14:55917400-55921400	Weak transcription	GM12878-XiMat	blood
16	chr14:55917800-55921000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:55918400-55920800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr14:55918600-55920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr14:55918600-55920600	Weak transcription	HMEC	breast
20	chr14:55918600-55920800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr14:55918600-55920800	Weak transcription	Brain Hippocampus Middle	brain
22	chr14:55918600-55920800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr14:55918800-55920600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:55918800-55920600	Weak transcription	Adipose Nuclei	Adipose
25	chr14:55918800-55920600	Weak transcription	Stomach Mucosa	stomach
26	chr14:55918800-55920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:55918800-55920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:55918800-55920800	Weak transcription	Fetal Stomach	stomach
29	chr14:55918800-55921000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:55918800-55921000	Weak transcription	Fetal Muscle Leg	muscle
31	chr14:55918800-55921000	Weak transcription	Pancreas	Pancrea
32	chr14:55918800-55921200	Weak transcription	Right Atrium	heart
33	chr14:55919000-55920600	Weak transcription	NH-A	brain
34	chr14:55919000-55920800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr14:55919000-55920800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:55919000-55920800	Weak transcription	Colonic Mucosa	Colon
37	chr14:55919000-55920800	Weak transcription	NHDF-Ad	bronchial
38	chr14:55919000-55921000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr14:55919000-55921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:55919000-55921200	Weak transcription	Esophagus	oesophagus
41	chr14:55919000-55921200	Weak transcription	Left Ventricle	heart
42	chr14:55919200-55920600	Weak transcription	NHLF	lung
43	chr14:55919400-55921000	Weak transcription	Osteobl	bone
44	chr14:55919800-55921000	Enhancers	Ovary	ovary
45	chr14:55920200-55920800	Enhancers	Hela-S3	cervix
46	chr14:55920200-55921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:55920400-55920600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr14:55920400-55920800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr14:55920400-55920800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr14:55920400-55920800	Enhancers	A549	lung

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